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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T46","span":{"begin":184,"end":190},"obj":"Body_part"},{"id":"T47","span":{"begin":1437,"end":1460},"obj":"Body_part"}],"attributes":[{"id":"A46","pred":"fma_id","subj":"T46","obj":"http://purl.org/sig/ont/fma/fma228738"},{"id":"A47","pred":"fma_id","subj":"T47","obj":"http://purl.org/sig/ont/fma/fma45661"}],"text":"Several studies from China reported high rates of Aspergillus infections among COVID-19 patients. In one study from the Jiangsu province in China, 60/257 COVID-19 (23.3%) patients had throat swab samples that tested positive for Aspergillus spp. and were reported as Aspergillus co-infections [8]. In another Chinese study from the Zhejiang province 8 of the 104 patients with COVID-19 (7.7%) patients were reported to have IPA although questions remain regarding criteria used for diagnosing IPA in this study (authors state EORTC/MSG criteria were used but all 8 patients seemingly lacked host factors) [71]. Another study from China reported that 27% of the COVID-19 patients (13/48) developed fungal infections but lacked further details [7]. In other reports from China, lower rates of fungal infections were reported ranging between 3.2–5% [54,55,72]. None of those studies have used specific definitions and standardized diagnostic algorithms to identify and define CAPA. In fact, diagnosis of pulmonary aspergillosis is challenging with culture exhibiting limited sensitivity [73,74], and galactomannan testing—the current gold standard—is rarely available in China [75]. As a result, some of these reported rates are likely an underestimate of the real burden of IPA in patients with COVID-19 requiring ICU admission, while other rates may be an overestimation due to potentially misinterpreting Aspergillus colonization in the upper respiratory tract as Aspergillus infection."}

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T13","span":{"begin":184,"end":190},"obj":"Body_part"},{"id":"T14","span":{"begin":1437,"end":1460},"obj":"Body_part"},{"id":"T15","span":{"begin":1443,"end":1460},"obj":"Body_part"}],"attributes":[{"id":"A13","pred":"uberon_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/UBERON_0000341"},{"id":"A14","pred":"uberon_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/UBERON_0001557"},{"id":"A15","pred":"uberon_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/UBERON_0000065"}],"text":"Several studies from China reported high rates of Aspergillus infections among COVID-19 patients. In one study from the Jiangsu province in China, 60/257 COVID-19 (23.3%) patients had throat swab samples that tested positive for Aspergillus spp. and were reported as Aspergillus co-infections [8]. In another Chinese study from the Zhejiang province 8 of the 104 patients with COVID-19 (7.7%) patients were reported to have IPA although questions remain regarding criteria used for diagnosing IPA in this study (authors state EORTC/MSG criteria were used but all 8 patients seemingly lacked host factors) [71]. Another study from China reported that 27% of the COVID-19 patients (13/48) developed fungal infections but lacked further details [7]. In other reports from China, lower rates of fungal infections were reported ranging between 3.2–5% [54,55,72]. None of those studies have used specific definitions and standardized diagnostic algorithms to identify and define CAPA. In fact, diagnosis of pulmonary aspergillosis is challenging with culture exhibiting limited sensitivity [73,74], and galactomannan testing—the current gold standard—is rarely available in China [75]. As a result, some of these reported rates are likely an underestimate of the real burden of IPA in patients with COVID-19 requiring ICU admission, while other rates may be an overestimation due to potentially misinterpreting Aspergillus colonization in the upper respiratory tract as Aspergillus infection."}

LitCovid-PubTator

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T162","span":{"begin":62,"end":72},"obj":"Disease"},{"id":"T163","span":{"begin":79,"end":87},"obj":"Disease"},{"id":"T164","span":{"begin":154,"end":162},"obj":"Disease"},{"id":"T165","span":{"begin":282,"end":292},"obj":"Disease"},{"id":"T166","span":{"begin":377,"end":385},"obj":"Disease"},{"id":"T167","span":{"begin":661,"end":669},"obj":"Disease"},{"id":"T168","span":{"begin":697,"end":714},"obj":"Disease"},{"id":"T169","span":{"begin":791,"end":808},"obj":"Disease"},{"id":"T170","span":{"begin":973,"end":977},"obj":"Disease"},{"id":"T171","span":{"begin":1011,"end":1024},"obj":"Disease"},{"id":"T172","span":{"begin":1293,"end":1301},"obj":"Disease"},{"id":"T173","span":{"begin":1476,"end":1485},"obj":"Disease"}],"attributes":[{"id":"A162","pred":"mondo_id","subj":"T162","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A163","pred":"mondo_id","subj":"T163","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A164","pred":"mondo_id","subj":"T164","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A165","pred":"mondo_id","subj":"T165","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A166","pred":"mondo_id","subj":"T166","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A167","pred":"mondo_id","subj":"T167","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A168","pred":"mondo_id","subj":"T168","obj":"http://purl.obolibrary.org/obo/MONDO_0002041"},{"id":"A169","pred":"mondo_id","subj":"T169","obj":"http://purl.obolibrary.org/obo/MONDO_0002041"},{"id":"A170","pred":"mondo_id","subj":"T170","obj":"http://purl.obolibrary.org/obo/MONDO_0007163"},{"id":"A171","pred":"mondo_id","subj":"T171","obj":"http://purl.obolibrary.org/obo/MONDO_0005657"},{"id":"A172","pred":"mondo_id","subj":"T172","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A173","pred":"mondo_id","subj":"T173","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"}],"text":"Several studies from China reported high rates of Aspergillus infections among COVID-19 patients. In one study from the Jiangsu province in China, 60/257 COVID-19 (23.3%) patients had throat swab samples that tested positive for Aspergillus spp. and were reported as Aspergillus co-infections [8]. In another Chinese study from the Zhejiang province 8 of the 104 patients with COVID-19 (7.7%) patients were reported to have IPA although questions remain regarding criteria used for diagnosing IPA in this study (authors state EORTC/MSG criteria were used but all 8 patients seemingly lacked host factors) [71]. Another study from China reported that 27% of the COVID-19 patients (13/48) developed fungal infections but lacked further details [7]. In other reports from China, lower rates of fungal infections were reported ranging between 3.2–5% [54,55,72]. None of those studies have used specific definitions and standardized diagnostic algorithms to identify and define CAPA. In fact, diagnosis of pulmonary aspergillosis is challenging with culture exhibiting limited sensitivity [73,74], and galactomannan testing—the current gold standard—is rarely available in China [75]. As a result, some of these reported rates are likely an underestimate of the real burden of IPA in patients with COVID-19 requiring ICU admission, while other rates may be an overestimation due to potentially misinterpreting Aspergillus colonization in the upper respiratory tract as Aspergillus infection."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T123","span":{"begin":209,"end":215},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T124","span":{"begin":606,"end":608},"obj":"http://purl.obolibrary.org/obo/CLO_0054055"},{"id":"T125","span":{"begin":650,"end":652},"obj":"http://purl.obolibrary.org/obo/CLO_0050509"},{"id":"T126","span":{"begin":683,"end":685},"obj":"http://purl.obolibrary.org/obo/CLO_0001382"},{"id":"T127","span":{"begin":1111,"end":1118},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T128","span":{"begin":1183,"end":1184},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T129","span":{"begin":1417,"end":1429},"obj":"http://purl.obolibrary.org/obo/UBERON_0001155"}],"text":"Several studies from China reported high rates of Aspergillus infections among COVID-19 patients. In one study from the Jiangsu province in China, 60/257 COVID-19 (23.3%) patients had throat swab samples that tested positive for Aspergillus spp. and were reported as Aspergillus co-infections [8]. In another Chinese study from the Zhejiang province 8 of the 104 patients with COVID-19 (7.7%) patients were reported to have IPA although questions remain regarding criteria used for diagnosing IPA in this study (authors state EORTC/MSG criteria were used but all 8 patients seemingly lacked host factors) [71]. Another study from China reported that 27% of the COVID-19 patients (13/48) developed fungal infections but lacked further details [7]. In other reports from China, lower rates of fungal infections were reported ranging between 3.2–5% [54,55,72]. None of those studies have used specific definitions and standardized diagnostic algorithms to identify and define CAPA. In fact, diagnosis of pulmonary aspergillosis is challenging with culture exhibiting limited sensitivity [73,74], and galactomannan testing—the current gold standard—is rarely available in China [75]. As a result, some of these reported rates are likely an underestimate of the real burden of IPA in patients with COVID-19 requiring ICU admission, while other rates may be an overestimation due to potentially misinterpreting Aspergillus colonization in the upper respiratory tract as Aspergillus infection."}

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T88","span":{"begin":424,"end":427},"obj":"Chemical"},{"id":"T90","span":{"begin":493,"end":496},"obj":"Chemical"},{"id":"T92","span":{"begin":532,"end":535},"obj":"Chemical"},{"id":"T94","span":{"begin":1097,"end":1110},"obj":"Chemical"},{"id":"T95","span":{"begin":1131,"end":1135},"obj":"Chemical"},{"id":"T97","span":{"begin":1272,"end":1275},"obj":"Chemical"}],"attributes":[{"id":"A88","pred":"chebi_id","subj":"T88","obj":"http://purl.obolibrary.org/obo/CHEBI_17824"},{"id":"A89","pred":"chebi_id","subj":"T88","obj":"http://purl.obolibrary.org/obo/CHEBI_30802"},{"id":"A90","pred":"chebi_id","subj":"T90","obj":"http://purl.obolibrary.org/obo/CHEBI_17824"},{"id":"A91","pred":"chebi_id","subj":"T90","obj":"http://purl.obolibrary.org/obo/CHEBI_30802"},{"id":"A92","pred":"chebi_id","subj":"T92","obj":"http://purl.obolibrary.org/obo/CHEBI_64220"},{"id":"A93","pred":"chebi_id","subj":"T92","obj":"http://purl.obolibrary.org/obo/CHEBI_64243"},{"id":"A94","pred":"chebi_id","subj":"T94","obj":"http://purl.obolibrary.org/obo/CHEBI_27680"},{"id":"A95","pred":"chebi_id","subj":"T95","obj":"http://purl.obolibrary.org/obo/CHEBI_29287"},{"id":"A96","pred":"chebi_id","subj":"T95","obj":"http://purl.obolibrary.org/obo/CHEBI_30050"},{"id":"A97","pred":"chebi_id","subj":"T97","obj":"http://purl.obolibrary.org/obo/CHEBI_17824"},{"id":"A98","pred":"chebi_id","subj":"T97","obj":"http://purl.obolibrary.org/obo/CHEBI_30802"}],"text":"Several studies from China reported high rates of Aspergillus infections among COVID-19 patients. In one study from the Jiangsu province in China, 60/257 COVID-19 (23.3%) patients had throat swab samples that tested positive for Aspergillus spp. and were reported as Aspergillus co-infections [8]. In another Chinese study from the Zhejiang province 8 of the 104 patients with COVID-19 (7.7%) patients were reported to have IPA although questions remain regarding criteria used for diagnosing IPA in this study (authors state EORTC/MSG criteria were used but all 8 patients seemingly lacked host factors) [71]. Another study from China reported that 27% of the COVID-19 patients (13/48) developed fungal infections but lacked further details [7]. In other reports from China, lower rates of fungal infections were reported ranging between 3.2–5% [54,55,72]. None of those studies have used specific definitions and standardized diagnostic algorithms to identify and define CAPA. In fact, diagnosis of pulmonary aspergillosis is challenging with culture exhibiting limited sensitivity [73,74], and galactomannan testing—the current gold standard—is rarely available in China [75]. As a result, some of these reported rates are likely an underestimate of the real burden of IPA in patients with COVID-19 requiring ICU admission, while other rates may be an overestimation due to potentially misinterpreting Aspergillus colonization in the upper respiratory tract as Aspergillus infection."}

LitCovid-PD-GlycoEpitope

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T2","span":{"begin":1097,"end":1110},"obj":"GlycoEpitope"}],"attributes":[{"id":"A2","pred":"glyco_epitope_db_id","subj":"T2","obj":"http://www.glycoepitope.jp/epitopes/EP0510"}],"text":"Several studies from China reported high rates of Aspergillus infections among COVID-19 patients. In one study from the Jiangsu province in China, 60/257 COVID-19 (23.3%) patients had throat swab samples that tested positive for Aspergillus spp. and were reported as Aspergillus co-infections [8]. In another Chinese study from the Zhejiang province 8 of the 104 patients with COVID-19 (7.7%) patients were reported to have IPA although questions remain regarding criteria used for diagnosing IPA in this study (authors state EORTC/MSG criteria were used but all 8 patients seemingly lacked host factors) [71]. Another study from China reported that 27% of the COVID-19 patients (13/48) developed fungal infections but lacked further details [7]. In other reports from China, lower rates of fungal infections were reported ranging between 3.2–5% [54,55,72]. None of those studies have used specific definitions and standardized diagnostic algorithms to identify and define CAPA. In fact, diagnosis of pulmonary aspergillosis is challenging with culture exhibiting limited sensitivity [73,74], and galactomannan testing—the current gold standard—is rarely available in China [75]. As a result, some of these reported rates are likely an underestimate of the real burden of IPA in patients with COVID-19 requiring ICU admission, while other rates may be an overestimation due to potentially misinterpreting Aspergillus colonization in the upper respiratory tract as Aspergillus infection."}

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T44","span":{"begin":424,"end":427},"obj":"Phenotype"},{"id":"T45","span":{"begin":493,"end":496},"obj":"Phenotype"},{"id":"T46","span":{"begin":1272,"end":1275},"obj":"Phenotype"}],"attributes":[{"id":"A44","pred":"hp_id","subj":"T44","obj":"http://purl.obolibrary.org/obo/HP_0020103"},{"id":"A45","pred":"hp_id","subj":"T45","obj":"http://purl.obolibrary.org/obo/HP_0020103"},{"id":"A46","pred":"hp_id","subj":"T46","obj":"http://purl.obolibrary.org/obo/HP_0020103"}],"text":"Several studies from China reported high rates of Aspergillus infections among COVID-19 patients. In one study from the Jiangsu province in China, 60/257 COVID-19 (23.3%) patients had throat swab samples that tested positive for Aspergillus spp. and were reported as Aspergillus co-infections [8]. In another Chinese study from the Zhejiang province 8 of the 104 patients with COVID-19 (7.7%) patients were reported to have IPA although questions remain regarding criteria used for diagnosing IPA in this study (authors state EORTC/MSG criteria were used but all 8 patients seemingly lacked host factors) [71]. Another study from China reported that 27% of the COVID-19 patients (13/48) developed fungal infections but lacked further details [7]. In other reports from China, lower rates of fungal infections were reported ranging between 3.2–5% [54,55,72]. None of those studies have used specific definitions and standardized diagnostic algorithms to identify and define CAPA. In fact, diagnosis of pulmonary aspergillosis is challenging with culture exhibiting limited sensitivity [73,74], and galactomannan testing—the current gold standard—is rarely available in China [75]. As a result, some of these reported rates are likely an underestimate of the real burden of IPA in patients with COVID-19 requiring ICU admission, while other rates may be an overestimation due to potentially misinterpreting Aspergillus colonization in the upper respiratory tract as Aspergillus infection."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T78","span":{"begin":0,"end":97},"obj":"Sentence"},{"id":"T79","span":{"begin":98,"end":297},"obj":"Sentence"},{"id":"T80","span":{"begin":298,"end":610},"obj":"Sentence"},{"id":"T81","span":{"begin":611,"end":746},"obj":"Sentence"},{"id":"T82","span":{"begin":747,"end":857},"obj":"Sentence"},{"id":"T83","span":{"begin":858,"end":978},"obj":"Sentence"},{"id":"T84","span":{"begin":979,"end":1179},"obj":"Sentence"},{"id":"T85","span":{"begin":1180,"end":1486},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Several studies from China reported high rates of Aspergillus infections among COVID-19 patients. In one study from the Jiangsu province in China, 60/257 COVID-19 (23.3%) patients had throat swab samples that tested positive for Aspergillus spp. and were reported as Aspergillus co-infections [8]. In another Chinese study from the Zhejiang province 8 of the 104 patients with COVID-19 (7.7%) patients were reported to have IPA although questions remain regarding criteria used for diagnosing IPA in this study (authors state EORTC/MSG criteria were used but all 8 patients seemingly lacked host factors) [71]. Another study from China reported that 27% of the COVID-19 patients (13/48) developed fungal infections but lacked further details [7]. In other reports from China, lower rates of fungal infections were reported ranging between 3.2–5% [54,55,72]. None of those studies have used specific definitions and standardized diagnostic algorithms to identify and define CAPA. In fact, diagnosis of pulmonary aspergillosis is challenging with culture exhibiting limited sensitivity [73,74], and galactomannan testing—the current gold standard—is rarely available in China [75]. As a result, some of these reported rates are likely an underestimate of the real burden of IPA in patients with COVID-19 requiring ICU admission, while other rates may be an overestimation due to potentially misinterpreting Aspergillus colonization in the upper respiratory tract as Aspergillus infection."}

2_test

{"project":"2_test","denotations":[{"id":"32599813-32503617-60095119","span":{"begin":606,"end":608},"obj":"32503617"},{"id":"32599813-32242738-60095120","span":{"begin":850,"end":852},"obj":"32242738"},{"id":"32599813-32311650-60095121","span":{"begin":853,"end":855},"obj":"32311650"},{"id":"32599813-31569472-60095122","span":{"begin":1085,"end":1087},"obj":"31569472"},{"id":"32599813-29036605-60095123","span":{"begin":1175,"end":1177},"obj":"29036605"}],"text":"Several studies from China reported high rates of Aspergillus infections among COVID-19 patients. In one study from the Jiangsu province in China, 60/257 COVID-19 (23.3%) patients had throat swab samples that tested positive for Aspergillus spp. and were reported as Aspergillus co-infections [8]. In another Chinese study from the Zhejiang province 8 of the 104 patients with COVID-19 (7.7%) patients were reported to have IPA although questions remain regarding criteria used for diagnosing IPA in this study (authors state EORTC/MSG criteria were used but all 8 patients seemingly lacked host factors) [71]. Another study from China reported that 27% of the COVID-19 patients (13/48) developed fungal infections but lacked further details [7]. In other reports from China, lower rates of fungal infections were reported ranging between 3.2–5% [54,55,72]. None of those studies have used specific definitions and standardized diagnostic algorithms to identify and define CAPA. In fact, diagnosis of pulmonary aspergillosis is challenging with culture exhibiting limited sensitivity [73,74], and galactomannan testing—the current gold standard—is rarely available in China [75]. As a result, some of these reported rates are likely an underestimate of the real burden of IPA in patients with COVID-19 requiring ICU admission, while other rates may be an overestimation due to potentially misinterpreting Aspergillus colonization in the upper respiratory tract as Aspergillus infection."}

PMC:7346000 / 14892-16378 JSONTXT

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PMC:7346000 / 14892-16378 JSON TXT